Bravo team's future is on the line when Commander Shaw (Peter Jessop) recommends they be split up, but Jason's unit has one final mission to prove him wrong.
The tension between Jason and Ray comes to a head, and Lisa faces her final test in officer candidate school.
Picking up after the explosive fall finale, Hodgins is eight weeks into his rehabilitation for his paralysis and forced to navigate life in a wheelchair. Meanwhile, Brennan and Booth investigate the death of a public defender who had multiple defendants from previous cases with motives to kill her.
Nell joins Deeks in the field on a case involving a former Marine who is being tracked by al-Qaida.
With the support of President Dalton, Elizabeth attempts to get the Senate's support for a history-making effort to lift the Cuban trade embargo. Also, Henry and Alison bond while touring Havana together.